Mercurial > repos > dereeper > sniplay
diff PedToFasta/pedToFasta.xml @ 10:c6640c49fd01 draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
author | dereeper |
---|---|
date | Mon, 16 Apr 2018 09:00:24 -0400 |
parents | 98c37a5d67f4 |
children |
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--- a/PedToFasta/pedToFasta.xml Wed Feb 07 22:08:47 2018 -0500 +++ b/PedToFasta/pedToFasta.xml Mon Apr 16 09:00:24 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="sniplay_pedToFasta" name="Ped2Fasta" version="1.0.0"> +<tool id="sniplay_pedToFasta" name="Ped2Fasta" version="2.0.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Convert PED file to Fasta File </description> @@ -34,7 +34,7 @@ <!-- [REQUIRED] Output files --> <outputs> - <data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" /> + <data name="fileout" format="fasta" label="${fileout_label}.fa" /> </outputs> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> @@ -47,7 +47,7 @@ </tests> <!-- [OPTIONAL] Help displayed in Galaxy --> - <help> + <help><![CDATA[ .. class:: infomark @@ -57,11 +57,11 @@ .. class:: infomark -**Galaxy integration** Andres Gwendoline, Institut Français de Bioinformatique. +**Galaxy integration** Provided by Southgreen & Andres Gwendoline (Institut Français de Bioinformatique) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Support** For any questions, please send an e-mail to support.abims@sb-roscoff.fr +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr --------------------------------------------------- @@ -73,29 +73,7 @@ Description ----------- - Convert PED file to Fasta File - ------------------ -Workflow position ------------------ - -**Upstream tool** - -=============== ========================== ======= -Name output file(s) format -=============== ========================== ======= -VCFtools Filter VCF file VCF -=============== ========================== ======= - - -**Downstream tool** - -=========== ========================== ======= -Name input file(s) format -=========== ========================== ======= -Readseq Fasta alignment fasta -=========== ========================== ======= - + | Convert PED file to Fasta File ---------- Input file @@ -104,16 +82,16 @@ PED file PED file usually from VCF tools ----------- -Parameters ----------- +--------- +Parameter +--------- Output file name Prefix for the output fasta file ------------- -Output files ------------- +----------- +Output file +----------- Fasta file PED file conversion @@ -124,8 +102,8 @@ Working example --------------- -Input files -=========== +Input file +========== PED file --------- @@ -134,13 +112,13 @@ CATB1 CATB1 0 0 0 0 C T T A C T A T A T A G G A -Parameters -========== +Parameter +========= Output name -> pedFile -Output files -============ +Output file +=========== pedFile.fa ---------- @@ -148,9 +126,7 @@ :: YWYWWRRSYYMKRRKMYRKSRKYRYRYKRKRSKKSYRWYSYRRYRRRWYWWYYWRRYRSRWSSRMYRRKSWMSKWRRYYWMYKYWRSYRWRYMWYYYMKYKYWRYRYRY - - - </help> + ]]></help> <citations> <!-- [HELP] As DOI or BibTex entry -->